Controlled Vocabularies and Ontologies

Help Index > Controlled Vocabularies and Ontologies

We strongly recommend using the following controlled vocabularies and data resources for data annotation:

Entity Resource Example ID Database URL MIRIAM URN
Protein UNIPROT P23470 http://www.uniprot.org/ urn:miriam:uniprot
Gene (human) HUGO Gene Nomenclature Committee (HGNC) HGNC:2674 http://www.genenames.org urn:miriam:hgnc
Gene (mouse) Mouse Genome Database (MGI) MGI:2442292 http://www.informatics.jax.org/ urn:miriam:mgd
Chemical ChEBI CHEBI:17234 http://www.ebi.ac.uk/chebi/ urn:miriam:obo.chebi
Chemical KEGG Compund C0003 http://www.genome.jp/kegg/compound/ urn:miriam:kegg.compound
Chemical PubChem 24749 http://pubchem.ncbi.nlm.nih.gov/ urn:miriam:pubchem.compound
Reaction Kinetics SABIO-RK 5046 http://sabio.h-its.org/ urn:miriam:sabiork.reaction
Enzymatic Activities Enzyme Nomenclature (EC) EC 1.14.13.39 http://www.ebi.ac.uk/intenz/ urn:miriam:ec-code
Pathways KEGG Pathways map00480 http://www.genome.jp/kegg/pathway.html urn:miriam:kegg.pathway
Reactions KEGG Reaction R00100 http://www.genome.jp/kegg/reaction/ urn:miriam:kegg.reaction
Reactions Rhea 12345 http://www.ebi.ac.uk/rhea/ urn:miriam:rhea
Reactions SABIO-RK Reactions 135 http://sabio.h-its.org/ urn:miriam:sabiork.reaction
Tissue Brenda Tissue Ontology (BTO) BTO:0002741 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013802/ urn:miriam:obo.bto
Cellular Location Gene Ontology GO:0005634 http://www.geneontology.org/ urn:miriam:obo.go
Molecular Function Gene Ontology GO:0046811 http://www.geneontology.org/ urn:miriam:obo.go
Biological Process Gene Ontology GO:0070365 http://www.geneontology.org/ urn:miriam:obo.go
Literature PubMed PMID:20738395 http://www.ncbi.nlm.nih.gov/pubmed/ urn:miriam:pubmed

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